I would like to use the capability of modeller to calculate different
kind of solvent accessibility data with the WRITE_DATA command. I can
get the *.psa file and the *.sol file using the script shown below
(practically identical with the example in the manual).
Now my questions:
o what are the units of the numbers given in the *.psa file?
I suppose that the "Sum" coloumns give the accessible surface in square
Angstrom. The "Per." coloumns are supposed to the accessible surface
area in percent of the total surface? Why do I get values above 100 in
many cases then?
o How should the ACCESSIBILITY_TYPE parameter of WRITE_DATA be used to
write different kind of accessibility dat to the Biso coloumn of the
*.sol file?
As far as I understand the manual the ACCESSIBILITY_TYPE parameter can
be used to influence this part of the *.sol output file? I tried various
things without any effect.
o What are the numbers written to the *.sol file with the script below?
Thanks a lot in advance,
Oliver
____________________________________________________________
Oliver Hucke (PostDoc)
Biomolecular Structure Center
Dept. of Biochemistry
University of Washington
Health Sciences Building K-418C
1959 NE Pacific Ave
Seattle, WA 98195
T:(206)685-7046
_______________________________
My input script:
------------------------------------------------------------
SET OUTPUT_CONTROL = 1 1 1 1 0
READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib'
SET HETATM_IO = off, WATER_IO = off
READ_MODEL FILE = 'protein'
SET RADII_FACTOR = 1.0
WRITE_DATA FILE = 'protein', OUTPUT = 'PSA'
--------------------------------------------------------------
Start of the protein.psa file:
--------------------------------------------------------------
#COLUMNS S S S N N N N N N N N N N
# produced by MODELLER
#
# File of summed (Sum) and % (per.) accessibilities
# probe radius : 1.400
# integration step : 0.100
# water included : ?
# hetatom included : ?
# accessibility type : CONTACT
# number of residues : 730
#
# Res Res All atoms Non P side Polar Side Total
Side Main Chain
# Num type Sum Per. Sum Per. Sum Per. Sum
Per. Sum Per.
ACCESS 55 PHE A 75.12 123.5 50.74 98.4 0.00 0.0 50.74
98.4 24.38 262.7
ACCESS 56 LEU A 19.62 34.7 16.14 34.6 0.00 0.0 16.14
34.6 3.47 35.0
ACCESS 57 SER A 20.64 61.1 11.84 75.1 7.67 97.5 19.51
82.6 1.13 11.1
ACCESS 58 LEU A 3.76 6.6 2.99 6.4 0.00 0.0 2.99
6.4 0.76 7.7
ACCESS 59 ASP A 31.28 79.4 9.54 59.8 13.93 103.7 23.47
79.8 7.81 78.3
--------------------------------------------------------------------------------------------------
Start of the corresponding *.sol file:
---------------------------------------------------------
# produced by MODELLER
#
# File of atomic accessibilities
# probe radius : 1.400
# integration step : 0.100
# water included : ?
# hetatom included : ?
# accessibility type : CONTACT
# number of residues : 730
ATOM 1 N PHE A 55 107.149 -1.404 53.483 1.650 14.140
ATOM 2 CA PHE A 55 106.564 -2.771 53.570 1.800 1.890
ATOM 3 C PHE A 55 106.502 -3.415 52.180 1.800 1.008
ATOM 4 O PHE A 55 107.505 -3.970 51.725 1.550 9.229
ATOM 5 CB PHE A 55 105.182 -2.745 54.253 1.800 2.554
ATOM 6 CG PHE A 55 105.162 -3.402 55.622 1.800 0.319
ATOM 7 CD1 PHE A 55 104.233 -4.411 55.914 1.800 7.619
ATOM 8 CD2 PHE A 55 106.077 -3.026 56.615 1.800 4.669
ATOM 9 CE1 PHE A 55 104.214 -5.040 57.174 1.800 11.557
--